MCP Server - Atomscale Documentation

The Model Context Protocol (MCP) is an open standard for connecting AI applications to external systems. The Atomscale MCP server lets AI tools search, analyze, and manage your metrology data — RHEED, SEM, XPS, ellipsometry, Raman, photoluminescence, and more — directly, without leaving your assistant. Every request is scoped to your Atomscale account: tools act as you, within your organization, and respect the same permissions as the web app.

Endpoint

https://api.atomscale.ai/mcp/

The server speaks streamable-HTTP. The trailing slash is required.

Setup

On first connection your client opens a browser to sign in with your Atomscale account, then caches a token for subsequent requests. Headless clients can authenticate with an API key instead (see Authentication).

Claude Code
Claude Desktop / claude.ai
Cursor
Other

claude mcp add --transport http atomscale https://api.atomscale.ai/mcp/

Then run /mcp inside Claude Code to complete sign-in and list the tools.

Go to Settings → Connectors → Add custom connector, then enter:

https://api.atomscale.ai/mcp/

Approve the access request when prompted.

Add to ~/.cursor/mcp.json:

{
  "mcpServers": {
    "atomscale": {
      "url": "https://api.atomscale.ai/mcp/"
    }
  }
}

Most MCP clients accept a remote server via mcpServers config:

{
  "mcpServers": {
    "atomscale": {
      "url": "https://api.atomscale.ai/mcp/"
    }
  }
}

Clients that don’t support the interactive OAuth flow can send an API key as a Bearer token — see Authentication.

Authentication

OAuth (default)
API key (headless)

Interactive clients sign in through your browser on first connect. There’s nothing to configure — approve the access request and the client caches its token.

For CI, scripts, or clients without a browser, send your API key as a Bearer token:

{
  "mcpServers": {
    "atomscale": {
      "url": "https://api.atomscale.ai/mcp/",
      "headers": { "Authorization": "Bearer YOUR_API_KEY" }
    }
  }
}

Generate a key from the Atomscale Dashboard under User → Manage Account → Access.

Never commit your API key to version control. Use environment variables or a secrets manager.

Tools

Your assistant chooses which tools to call. Write tools (marked below) prompt for confirmation in most clients before making changes.

Tool	Access	Description
`search_data`	Read	Search the data catalogue
`fetch_data`	Read	Get one data item’s metadata by ID
`fetch_results`	Read	Processed analysis results or AI summary for a data item
`fetch_embeddings`	Read	Similarity embeddings for a data item
`search_sample`	Read	Search physical samples
`fetch_sample`	Read	Get one physical sample by ID
`list_notebooks`	Read	List your organization’s analysis notebooks
`annotate_data`	Write	Apply tags and/or attach a note to a data item
`create_notebook`	Write	Create an analysis notebook, optionally seeded with Python (marimo) source
`edit_notebook`	Write	Commit a new Python (marimo) source version to a notebook
`upload_data`	Write	Get presigned URLs to upload a new file
`start_stream`	Write	Start a timeseries stream
`push_stream_chunk`	Write	Push one chunk of points to an active stream
`stop_stream`	Write	Finalize a stream

Streaming

Streams let an instrument or agent send timeseries data point-by-point instead of uploading a finished file. start_stream opens a stream with a fixed chunk size (points_per_chunk) and returns its data_id. Push points with push_stream_chunk, one call per channel per chunk:

Every chunk must contain exactly points_per_chunk points. Only the final chunk before stop_stream may be shorter. Chunk length is not validated server-side, so a short chunk leaves a gap and an oversized chunk overwrites the start of the next slice.
timestamps are unix epoch seconds and pair 1:1 with values.
Chunks may arrive out of order, and retrying a (channel_name, chunk_index) pair replaces that slice, so retries are safe.
For multiple channels, call once per channel with the same chunk_index.

Call stop_stream once all chunks are pushed to finalize the stream and trigger processing.

A ping tool is also available for liveness checks and requires no authentication.

​Endpoint

​Setup

​Authentication

​Tools

​Streaming

Endpoint

Setup

Authentication

Tools

Streaming